Getting clipping sounds after cropping recorded audio.

When you cut or split the clips and want to delete it and do a new take or simply punch in over it.... be sure you select the clip by clicking it to highlight that entire clip. Once it's highlighted, you can delete the existing contents and then also set your auto punch in and out on that clip easily.
 
When you do it that way, you should NOT get any sort of audible click at the edit points. There will be no need to do cross fades to get it right. You might need a few tries to get the levels right if you're doing it on a different day and have changed your settings from the original session. If it's in the same session, it should be flawless the first time.
 
I use this method all the time and it works perfectly every time.
 
If you try to do the edit manually by selecting the in and out points, chances are very slim that you will get it perfect. As a result, you will hear the click or pop.